Toward a structome of Acinetobacter baumannii drug targets

Abstract

Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.

Keywords: X-ray structure; antibiotic resistance; antibiotic targets; gram-negative; structure based drug design.

Figure 1

(a) Superposition of chain A of human methionine tRNA synthetase (green, 5GL7) and A. baumannii methionine tRNA ligase (blue, 5URB). Key residues involved ATP, L‐methionine and tRNA binding sites are depicted as spheres. (b) Stereo images of A. baumannii methionine tRNA ligase active site (blue, 5URB). Significant differences in key residues from human methionine tRNA synthetase which can be exploited for drug design are highlighted (blue, A. baumannii MetRS; green, human MetRS)

Figure 2

Superposition of chain A of human uroporphyrinogen decarboxylase (blue, 3GW0) and A. baumannii uroporphyrinogen decarboxylase (tan, 4ZR8). Amino acids that have been highlighted are associated with key residues in uroporphyrinogen binding and subunit dimerization sites. Chloride (green) and magnesium (yellow) cofactors are shown as spheres. Residues associated with these essential functions are too similar to be considered for drug design. In addition, there exists no difference in tertiary structure to be exploited for drug design

Figure 3

Superposition of subunit A of human coproporphyrinogen III oxidase (blue, 2AEX) and A. baumannii coproporphyrinogen III oxidase (tan, 5EO6). Key residues involved in coproporphyrinogen III catalytic activity displayed. While these residues are too conserved or identical to yield specificity, there exists a divergent structure within the conformation of these two enzymes. Highlighted in yellow is an extended α‐helix of A. baumannii which encloses some solvent‐exposed active site residues. Highlighted in dark blue is the same sequence segment, but in the human ortholog it is a less structured helix that is shifted significantly

Figure 4

Superposition of subunit A of human methionine aminopeptidase 2 (blue, 4U1B) and A. baumannii methionine aminopeptidase (tan, 6MRF). Key residues involved in catalytic activity and metal binding are displayed with cobalt (II) cofactors (pink). Residues show high active site similarity with some differences arising from individual residue orientation

Figure 5

Superposition of chain A of human tyrosyl tRNA synthetase (blue, 5GL7) and A. baumannii tyrosyl tRNA ligase (tan, 5URB). Key residues involved in the binding sites of ATP, l‐tyrosine, and tRNA are highlighted showing divergence that might be exploited in selective antibiotic development. Some differences in highlighted in the discussion are not displayed due to gaps in pairwise alignment